TY - JOUR
T1 - Exploring the crop epigenome
T2 - a comparison of DNA methylation profiling techniques
AU - Agius, Dolores Rita
AU - Kapazoglou, Aliki
AU - Avramidou, Evangelia
AU - Baranek, Miroslav
AU - Carneros, Elena
AU - Caro, Elena
AU - Castiglione, Stefano
AU - Cicatelli, Angela
AU - Radanovic, Aleksandra
AU - Ebejer, Jean Paul
AU - Gackowski, Daniel
AU - Guarino, Francesco
AU - Gulyás, Andrea
AU - Hidvégi, Norbert
AU - Hoenicka, Hans
AU - Inácio, Vera
AU - Johannes, Frank
AU - Karalija, Erna
AU - Lieberman-Lazarovich, Michal
AU - Martinelli, Federico
AU - Maury, Stéphane
AU - Mladenov, Velimir
AU - Morais-Cecílio, Leonor
AU - Pecinka, Ales
AU - Tani, Eleni
AU - Testillano, Pilar S.
AU - Todorov, Dimitar
AU - Valledor, Luis
AU - Vassileva, Valya
N1 - Publisher Copyright:
Copyright © 2023 Agius, Kapazoglou, Avramidou, Baranek, Carneros, Caro, Castiglione, Cicatelli, Radanovic, Ebejer, Gackowski, Guarino, Gulyás, Hidvégi, Hoenicka, Inácio, Johannes, Karalija, Lieberman-Lazarovich, Martinelli, Maury, Mladenov, Morais-Cecílio, Pecinka, Tani, Testillano, Todorov, Valledor and Vassileva.
PY - 2023
Y1 - 2023
N2 - Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
AB - Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
KW - DNA methylation modulation
KW - DNA methylation profiling
KW - bisulfite sequencing
KW - crop epigenome
KW - immunological techniques
KW - mass spectrometry
KW - next-generation sequencing
UR - http://www.scopus.com/inward/record.url?scp=85161895018&partnerID=8YFLogxK
U2 - 10.3389/fpls.2023.1181039
DO - 10.3389/fpls.2023.1181039
M3 - Review article
AN - SCOPUS:85161895018
SN - 1664-462X
VL - 14
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 1181039
ER -